Defective return u/s 139 (9) for excess deductions of TDS by deductor

Dear Experts,

The question is that, how to correct a defective return u/s 139(9) in case where the TDS has been deducted twice by the deductor ( i.e. on advance payment and invoice credit) ? The gross receipts as per AIS or Form 26AS have not matched with the actual amount which is reported by the assessee in the ITR. The amount of TDS is more than the Gross Receipts so that the department has denied to get any refund for excess deductions.
please assist what is the correct procedure to overcome in this situation.

Thanks
Pradeep